Package evaluation of GigaSOM on Julia 1.13.0-DEV.853 (3e868b27cf*) started at 2025-07-17T03:58:55.682 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.66s ################################################################################ # Installation # Installing GigaSOM... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [a03a9c34] + GigaSOM v0.7.0 Updating `~/.julia/environments/v1.13/Manifest.toml` [66dad0bd] + AliasTables v1.1.3 [336ed68f] + CSV v0.10.15 [944b1d66] + CodecZlib v0.7.8 [34da2185] + Compat v4.17.0 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.16.0 [a93c6f00] + DataFrames v1.7.0 [864edb3b] + DataStructures v0.18.22 [e2d170a0] + DataValueInterfaces v1.0.0 [b4f34e82] + Distances v0.10.12 [aaf54ef3] + DistributedArrays v0.6.7 [f6a0035f] + DistributedData v0.2.0 [31c24e10] + Distributions v0.25.120 [ffbed154] + DocStringExtensions v0.9.5 ⌅ [d76558cf] + FCSFiles v0.1.5 [5789e2e9] + FileIO v1.17.0 [48062228] + FilePathsBase v0.9.24 [1a297f60] + FillArrays v1.13.0 [a03a9c34] + GigaSOM v0.7.0 [34004b35] + HypergeometricFunctions v0.3.28 [842dd82b] + InlineStrings v1.4.4 [18e54dd8] + IntegerMathUtils v0.1.3 [41ab1584] + InvertedIndices v1.3.1 [92d709cd] + IrrationalConstants v0.2.4 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [b964fa9f] + LaTeXStrings v1.4.0 [2ab3a3ac] + LogExpFunctions v0.3.29 [e1d29d7a] + Missings v1.2.0 [b8a86587] + NearestNeighbors v0.4.22 [bac558e1] + OrderedCollections v1.8.1 [90014a1f] + PDMats v0.11.35 [69de0a69] + Parsers v2.8.3 [2dfb63ee] + PooledArrays v1.4.3 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [08abe8d2] + PrettyTables v2.4.0 [27ebfcd6] + Primes v0.5.7 [43287f4e] + PtrArrays v1.3.0 [1fd47b50] + QuadGK v2.11.2 [189a3867] + Reexport v1.2.2 [ae029012] + Requires v1.3.1 [79098fc4] + Rmath v0.8.0 [91c51154] + SentinelArrays v1.4.8 [a2af1166] + SortingAlgorithms v1.2.1 [276daf66] + SpecialFunctions v2.5.1 [860ef19b] + StableRNGs v1.0.3 [90137ffa] + StaticArrays v1.9.14 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [82ae8749] + StatsAPI v1.7.1 [2913bbd2] + StatsBase v0.34.5 [4c63d2b9] + StatsFuns v1.5.0 [892a3eda] + StringManipulation v0.4.1 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [3bb67fe8] + TranscodingStreams v0.11.3 [ea10d353] + WeakRefStrings v1.4.2 [76eceee3] + WorkerUtilities v1.6.1 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [f50d1b31] + Rmath_jll v0.5.1+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.12.0 [f489334b] + StyledStrings v1.11.0 [4607b0f0] + SuiteSparse [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [8dfed614] + Test v1.11.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.14.1+1 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.5.20 [4536629a] + OpenBLAS_jll v0.3.29+0 [05823500] + OpenLibm_jll v0.8.5+0 [458c3c95] + OpenSSL_jll v3.5.1+0 [efcefdf7] + PCRE2_jll v10.45.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 4.48s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 66.86s ################################################################################ # Testing # Testing GigaSOM Status `/tmp/jl_1pYRNA/Project.toml` [336ed68f] CSV v0.10.15 [a93c6f00] DataFrames v1.7.0 [b4f34e82] Distances v0.10.12 [aaf54ef3] DistributedArrays v0.6.7 [f6a0035f] DistributedData v0.2.0 [31c24e10] Distributions v0.25.120 ⌅ [d76558cf] FCSFiles v0.1.5 [5789e2e9] FileIO v1.17.0 [a03a9c34] GigaSOM v0.7.0 [682c06a0] JSON v0.21.4 [b8a86587] NearestNeighbors v0.4.22 [860ef19b] StableRNGs v1.0.3 ⌅ [fdbf4ff8] XLSX v0.7.10 [8ba89e20] Distributed v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_1pYRNA/Manifest.toml` [66dad0bd] AliasTables v1.1.3 [336ed68f] CSV v0.10.15 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.17.0 [a8cc5b0e] Crayons v4.1.1 [9a962f9c] DataAPI v1.16.0 [a93c6f00] DataFrames v1.7.0 [864edb3b] DataStructures v0.18.22 [e2d170a0] DataValueInterfaces v1.0.0 [b4f34e82] Distances v0.10.12 [aaf54ef3] DistributedArrays v0.6.7 [f6a0035f] DistributedData v0.2.0 [31c24e10] Distributions v0.25.120 [ffbed154] DocStringExtensions v0.9.5 [8f5d6c58] EzXML v1.2.1 ⌅ [d76558cf] FCSFiles v0.1.5 [5789e2e9] FileIO v1.17.0 [48062228] FilePathsBase v0.9.24 [1a297f60] FillArrays v1.13.0 [a03a9c34] GigaSOM v0.7.0 [34004b35] HypergeometricFunctions v0.3.28 [842dd82b] InlineStrings v1.4.4 [18e54dd8] IntegerMathUtils v0.1.3 [41ab1584] InvertedIndices v1.3.1 [92d709cd] IrrationalConstants v0.2.4 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [682c06a0] JSON v0.21.4 [b964fa9f] LaTeXStrings v1.4.0 [2ab3a3ac] LogExpFunctions v0.3.29 [e1d29d7a] Missings v1.2.0 [b8a86587] NearestNeighbors v0.4.22 [bac558e1] OrderedCollections v1.8.1 [90014a1f] PDMats v0.11.35 [69de0a69] Parsers v2.8.3 [2dfb63ee] PooledArrays v1.4.3 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [08abe8d2] PrettyTables v2.4.0 [27ebfcd6] Primes v0.5.7 [43287f4e] PtrArrays v1.3.0 [1fd47b50] QuadGK v2.11.2 [189a3867] Reexport v1.2.2 [ae029012] Requires v1.3.1 [79098fc4] Rmath v0.8.0 [91c51154] SentinelArrays v1.4.8 [a2af1166] SortingAlgorithms v1.2.1 [276daf66] SpecialFunctions v2.5.1 [860ef19b] StableRNGs v1.0.3 [90137ffa] StaticArrays v1.9.14 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [82ae8749] StatsAPI v1.7.1 [2913bbd2] StatsBase v0.34.5 [4c63d2b9] StatsFuns v1.5.0 [892a3eda] StringManipulation v0.4.1 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [ea10d353] WeakRefStrings v1.4.2 [76eceee3] WorkerUtilities v1.6.1 ⌅ [fdbf4ff8] XLSX v0.7.10 ⌅ [a5390f91] ZipFile v0.9.4 [94ce4f54] Libiconv_jll v1.18.0+0 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [f50d1b31] Rmath_jll v0.5.1+0 ⌅ [02c8fc9c] XML2_jll v2.13.6+1 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [9fa8497b] Future v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.12.0 [f489334b] StyledStrings v1.11.0 [4607b0f0] SuiteSparse [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.14.1+1 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.5.20 [4536629a] OpenBLAS_jll v0.3.29+0 [05823500] OpenLibm_jll v0.8.5+0 [458c3c95] OpenSSL_jll v3.5.1+0 [efcefdf7] PCRE2_jll v10.45.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... Precompiling packages... 6787.7 ms ✓ XLSX 1 dependency successfully precompiled in 7 seconds. 17 already precompiled. Precompiling packages... 4739.3 ms ✓ Distributions → DistributionsTestExt 1 dependency successfully precompiled in 6 seconds. 49 already precompiled. ┌ Warning: Base.download is deprecated; use Downloads.download instead │ caller = top-level scope at testLoadPBMC8.jl:33 └ @ Core ~/.julia/packages/GigaSOM/RWenv/test/testLoadPBMC8.jl:33 Archive: PBMC8_fcs_files.zip inflating: PBMC8_30min_patient1_BCR-XL.fcs inflating: PBMC8_30min_patient1_Reference.fcs inflating: PBMC8_30min_patient2_BCR-XL.fcs inflating: PBMC8_30min_patient2_Reference.fcs inflating: PBMC8_30min_patient3_BCR-XL.fcs inflating: PBMC8_30min_patient3_Reference.fcs inflating: PBMC8_30min_patient4_BCR-XL.fcs inflating: PBMC8_30min_patient4_Reference.fcs inflating: PBMC8_30min_patient5_BCR-XL.fcs inflating: PBMC8_30min_patient5_Reference.fcs inflating: PBMC8_30min_patient6_BCR-XL.fcs inflating: PBMC8_30min_patient6_Reference.fcs inflating: PBMC8_30min_patient7_BCR-XL.fcs inflating: PBMC8_30min_patient7_Reference.fcs inflating: PBMC8_30min_patient8_BCR-XL.fcs inflating: PBMC8_30min_patient8_Reference.fcs ┌ Warning: `type` keyword argument is deprecated; a single type can be passed to `types` instead └ @ CSV ~/.julia/packages/CSV/XLcqT/src/context.jl:356 ┌ Warning: `type` keyword argument is deprecated; a single type can be passed to `types` instead └ @ CSV ~/.julia/packages/CSV/XLcqT/src/context.jl:356 ┌ Warning: `type` keyword argument is deprecated; a single type can be passed to `types` instead └ @ CSV ~/.julia/packages/CSV/XLcqT/src/context.jl:356 ┌ Warning: `type` keyword argument is deprecated; a single type can be passed to `types` instead └ @ CSV ~/.julia/packages/CSV/XLcqT/src/context.jl:356 ┌ Warning: `type` keyword argument is deprecated; a single type can be passed to `types` instead └ @ CSV ~/.julia/packages/CSV/XLcqT/src/context.jl:356 ┌ Warning: `type` keyword argument is deprecated; a single type can be passed to `types` instead └ @ CSV ~/.julia/packages/CSV/XLcqT/src/context.jl:356 ┌ Warning: `type` keyword argument is deprecated; a single type can be passed to `types` instead └ @ CSV ~/.julia/packages/CSV/XLcqT/src/context.jl:356 From worker 7: ┌ Warning: `type` keyword argument is deprecated; a single type can be passed to `types` instead From worker 7: └ @ CSV ~/.julia/packages/CSV/XLcqT/src/context.jl:356 From worker 6: ┌ Warning: `type` keyword argument is deprecated; a single type can be passed to `types` instead From worker 6: └ @ CSV ~/.julia/packages/CSV/XLcqT/src/context.jl:356 From worker 8: ┌ Warning: `type` keyword argument is deprecated; a single type can be passed to `types` instead From worker 8: └ @ CSV ~/.julia/packages/CSV/XLcqT/src/context.jl:356 From worker 7: ┌ Warning: `type` keyword argument is deprecated; a single type can be passed to `types` instead From worker 7: └ @ CSV ~/.julia/packages/CSV/XLcqT/src/context.jl:356 File splitting: Error During Test at /home/pkgeval/.julia/packages/GigaSOM/RWenv/test/testFileSplitting.jl:1 Got exception outside of a @test TaskFailedException nested task error: worker did not connect within 60.0 seconds Stacktrace: [1] error(s::String) @ Base ./error.jl:44 [2] create_worker(manager::Distributed.LocalManager, wconfig::WorkerConfig) @ Distributed /opt/julia/share/julia/stdlib/v1.13/Distributed/src/cluster.jl:709 [3] setup_launched_worker(manager::Distributed.LocalManager, wconfig::WorkerConfig, launched_q::Vector{Int64}) @ Distributed /opt/julia/share/julia/stdlib/v1.13/Distributed/src/cluster.jl:555 [4] (::Distributed.var"#39#40"{Distributed.LocalManager, Vector{Int64}, WorkerConfig})() @ Distributed /opt/julia/share/julia/stdlib/v1.13/Distributed/src/cluster.jl:511 ...and 7 more exceptions. Stacktrace: [1] sync_end(c::Channel{Any}) @ Base ./task.jl:601 [2] macro expansion @ ./task.jl:634 [inlined] [3] addprocs_locked(manager::Distributed.LocalManager; kwargs::@Kwargs{}) @ Distributed /opt/julia/share/julia/stdlib/v1.13/Distributed/src/cluster.jl:496 [4] addprocs_locked @ /opt/julia/share/julia/stdlib/v1.13/Distributed/src/cluster.jl:461 [inlined] [5] addprocs(manager::Distributed.LocalManager; kwargs::@Kwargs{}) @ Distributed /opt/julia/share/julia/stdlib/v1.13/Distributed/src/cluster.jl:455 [6] addprocs @ /opt/julia/share/julia/stdlib/v1.13/Distributed/src/cluster.jl:448 [inlined] [7] #addprocs#197 @ /opt/julia/share/julia/stdlib/v1.13/Distributed/src/managers.jl:472 [inlined] [8] addprocs(np::Int64) @ Distributed /opt/julia/share/julia/stdlib/v1.13/Distributed/src/managers.jl:469 [9] top-level scope @ ~/.julia/packages/GigaSOM/RWenv/test/testFileSplitting.jl:3 [10] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined] [11] macro expansion @ ~/.julia/packages/GigaSOM/RWenv/test/testFileSplitting.jl:3 [inlined] [12] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [13] top-level scope @ ~/.julia/packages/GigaSOM/RWenv/test/runtests.jl:21 [14] macro expansion @ /opt/julia/share/julia/stdlib/v1.13/Test/src/Test.jl:1855 [inlined] [15] macro expansion @ ~/.julia/packages/GigaSOM/RWenv/test/runtests.jl:33 [inlined] [16] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [17] top-level scope @ none:6 [18] eval(m::Module, e::Any) @ Core ./boot.jl:489 [19] exec_options(opts::Base.JLOptions) @ Base ./client.jl:286 [20] _start() @ Base ./client.jl:553 Test Summary: | Pass Error Total Time GigaSOM test suite | 54 1 55 11m29.7s High-level operations on distributed data | 2 2 1m38.8s SOM training helper functions | 15 15 6.4s Dataset splitting helpers | 10 10 1.8s File loading with compensation | 1 1 23.2s load-time columns normalization | 1 1 1.6s Single-CPU batch processing | 9 9 1m02.9s Parallel processing | 8 8 1m14.8s CSV loading | 8 8 4m32.9s File splitting | 1 1 1m35.4s RNG of the outermost testset: Xoshiro(0xe7746035402769bf, 0x5d7257b41a464612, 0x5ca31778fb82a386, 0x1e08790b6c7b6790, 0xa1362bfe6fe74283) ERROR: LoadError: Some tests did not pass: 54 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/GigaSOM/RWenv/test/runtests.jl:20 ┌ Warning: Forcibly interrupting busy workers │ exception = rmprocs: pids [9, 10, 11, 12, 13, 14, 15, 16] not terminated after 5.0 seconds. └ @ Distributed /opt/julia/share/julia/stdlib/v1.13/Distributed/src/cluster.jl:1269 ┌ Warning: rmprocs: process 1 not removed └ @ Distributed /opt/julia/share/julia/stdlib/v1.13/Distributed/src/cluster.jl:1065 Testing failed after 644.0s ERROR: LoadError: Package GigaSOM errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2446 [3] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2301 [inlined] [4] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:500 [5] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:164 [6] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [7] test @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:152 [inlined] [8] #test#81 @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:151 [inlined] [9] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:219 [10] include(mod::Module, _path::String) @ Base ./Base.jl:309 [11] exec_options(opts::Base.JLOptions) @ Base ./client.jl:320 [12] _start() @ Base ./client.jl:553 in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 PkgEval failed after 854.51s: package tests unexpectedly errored